data_4K5Y
#
_model_server_result.job_id            c_dQpF1y1cCplHUzNYsfMg 
_model_server_result.datetime_utc      '2024-11-14 13:15:36' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          4k5y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":504}' 
#
_entry.id    4K5Y 
#
_exptl.entry_id    4K5Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            4K5Y 
_cell.length_a            86.559 
_cell.length_b            123.968 
_cell.length_c            166.834 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4K5Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,T 1 1 
B,I,J,K,L,M,N,O,P,Q,U 2 1 
C,R,S 3 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 K N N 
? 6 L N N 
? 6 M N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 A SG CYS 86 A CYS 188 1_555 A SG CYS 313 A CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf2 B SG CYS 86 B CYS 188 1_555 B SG CYS 313 B CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
disulf ? disulf3 C SG CYS 86 C CYS 188 1_555 C SG CYS 313 C CYS 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
#
_chem_comp.formula           'C40 H77 O10 P' 
_chem_comp.formula_weight    749.007 
_chem_comp.id                PGW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)];PHOSPHATIDYLGLYCEROL 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
CAD C05 PGW sing 446 n n 
CAD HAD PGW sing 447 n n 
CAD HADA PGW sing 448 n n 
OAE CAD PGW sing 449 n n 
OAE HOAE PGW sing 450 n n 
OAF C05 PGW sing 451 n n 
OAF HOAF PGW sing 452 n n 
P O13 PGW sing 453 n n 
P O11 PGW sing 454 n n 
C01 O03 PGW sing 455 n n 
C01 C02 PGW sing 456 n n 
C01 H01 PGW sing 457 n n 
C01 H01A PGW sing 458 n n 
C1 C2 PGW sing 459 n n 
O01 C1 PGW sing 460 n n 
C02 O01 PGW sing 461 n n 
C02 H02 PGW sing 462 n n 
C2 C3 PGW sing 463 n n 
C2 H2 PGW sing 464 n n 
C2 H2A PGW sing 465 n n 
O02 C1 PGW doub 466 n n 
C03 C02 PGW sing 467 n n 
C03 H03 PGW sing 468 n n 
C03 H03A PGW sing 469 n n 
C3 C4 PGW sing 470 n n 
C3 H3 PGW sing 471 n n 
C3 H3A PGW sing 472 n n 
C04 C05 PGW sing 473 n n 
C04 O12 PGW sing 474 n n 
C04 H04 PGW sing 475 n n 
C04 H04A PGW sing 476 n n 
C4 C5 PGW sing 477 n n 
C4 H4 PGW sing 478 n n 
C4 H4A PGW sing 479 n n 
O04 C19 PGW doub 480 n n 
C05 H05 PGW sing 481 n n 
C5 C6 PGW sing 482 n n 
C5 H5 PGW sing 483 n n 
C5 H5A PGW sing 484 n n 
C06 C07 PGW sing 485 n n 
C06 H06 PGW sing 486 n n 
C06 H06A PGW sing 487 n n 
C6 C7 PGW sing 488 n n 
C6 H6 PGW sing 489 n n 
C6 H6A PGW sing 490 n n 
C07 H07 PGW sing 491 n n 
C07 H07A PGW sing 492 n n 
C7 C8 PGW sing 493 n n 
C7 H7 PGW sing 494 n n 
C7 H7A PGW sing 495 n n 
C08 C07 PGW sing 496 n n 
C08 H08 PGW sing 497 n n 
C08 H08A PGW sing 498 n n 
C8 C9 PGW sing 499 n n 
C8 H8 PGW sing 500 n n 
C8 H8A PGW sing 501 n n 
C09 C08 PGW sing 502 n n 
C09 C11 PGW sing 503 n n 
C09 H09 PGW sing 504 n n 
C09 H09A PGW sing 505 n n 
C9 C10 PGW doub 506 z n 
C10 C06 PGW sing 507 n n 
C11 H11 PGW sing 508 n n 
C11 H11A PGW sing 509 n n 
O11 C03 PGW sing 510 n n 
C12 C11 PGW sing 511 n n 
C12 H12 PGW sing 512 n n 
C12 H12A PGW sing 513 n n 
O12 P PGW sing 514 n n 
C13 C12 PGW sing 515 n n 
C13 C14 PGW sing 516 n n 
C13 H13 PGW sing 517 n n 
C13 H13A PGW sing 518 n n 
O13 HO13 PGW sing 519 n n 
C14 H14 PGW sing 520 n n 
C14 H14A PGW sing 521 n n 
C14 H14B PGW sing 522 n n 
O14 P PGW doub 523 n n 
C15 C16 PGW sing 524 n n 
C15 H15 PGW sing 525 n n 
C15 H15A PGW sing 526 n n 
C16 H16 PGW sing 527 n n 
C16 H16A PGW sing 528 n n 
C17 C16 PGW sing 529 n n 
C17 C18 PGW sing 530 n n 
C17 H17 PGW sing 531 n n 
C17 H17A PGW sing 532 n n 
C18 C28 PGW sing 533 n n 
C18 H18 PGW sing 534 n n 
C18 H18A PGW sing 535 n n 
C19 O03 PGW sing 536 n n 
C19 C20 PGW sing 537 n n 
C20 C21 PGW sing 538 n n 
C20 H20 PGW sing 539 n n 
C20 H20A PGW sing 540 n n 
C21 C22 PGW sing 541 n n 
C21 H21 PGW sing 542 n n 
C21 H21A PGW sing 543 n n 
C22 C23 PGW sing 544 n n 
C22 H22 PGW sing 545 n n 
C22 H22A PGW sing 546 n n 
C23 C24 PGW sing 547 n n 
C23 H23 PGW sing 548 n n 
C23 H23A PGW sing 549 n n 
C24 C25 PGW sing 550 n n 
C24 H24 PGW sing 551 n n 
C24 H24A PGW sing 552 n n 
C25 C26 PGW sing 553 n n 
C25 H25 PGW sing 554 n n 
C25 H25A PGW sing 555 n n 
C26 C27 PGW sing 556 n n 
C26 H26 PGW sing 557 n n 
C26 H26A PGW sing 558 n n 
C27 C15 PGW sing 559 n n 
C27 H27 PGW sing 560 n n 
C27 H27A PGW sing 561 n n 
C28 H28 PGW sing 562 n n 
C28 H28A PGW sing 563 n n 
C29 H29 PGW sing 564 n n 
C29 H29A PGW sing 565 n n 
C29 H29B PGW sing 566 n n 
C30 C28 PGW sing 567 n n 
C30 C29 PGW sing 568 n n 
C30 H30 PGW sing 569 n n 
C30 H30A PGW sing 570 n n 
C9 H9 PGW sing 571 n n 
C10 H10 PGW sing 572 n n 
#
_atom_sites.entry_id                     4K5Y 
_atom_sites.fract_transf_matrix[1][1]    0.011553 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008067 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.005994 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
D 2 1Q5 A 1 401 401 1Q5 1Q5 . 
E 3 OLA A 1 501 501 OLA OLA . 
F 4 OLC A 1 502 502 OLC OLC . 
G 4 OLC A 1 503 503 OLC OLC . 
H 5 SO4 A 1 504 504 SO4 SO4 . 
I 2 1Q5 B 1 401 401 1Q5 1Q5 . 
J 4 OLC B 1 501 501 OLC OLC . 
K 6 PGW B 1 502 502 PGW PGW . 
L 6 PGW B 1 503 503 PGW PGW . 
M 6 PGW B 1 504 504 PGW PGW . 
N 7 1PE B 1 505 505 1PE 1PE . 
O 5 SO4 B 1 506 506 SO4 SO4 . 
P 5 SO4 B 1 507 507 SO4 SO4 . 
Q 5 SO4 B 1 508 508 SO4 SO4 . 
R 2 1Q5 C 1 401 401 1Q5 1Q5 . 
S 3 OLA C 1 501 501 OLA OLA . 
T 8 HOH A 1 601 601 HOH HOH . 
T 8 HOH A 2 602 602 HOH HOH . 
T 8 HOH A 3 603 603 HOH HOH . 
T 8 HOH A 4 604 604 HOH HOH . 
U 8 HOH B 1 601 601 HOH HOH . 
U 8 HOH B 2 602 602 HOH HOH . 
U 8 HOH B 3 603 603 HOH HOH . 
U 8 HOH B 4 604 604 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C01 PGW . . . M 6 -32.159 11.364 10.081 1 74.99 ? C01 PGW 504 B 1 
HETATM 2 C C1 PGW . . . M 6 -34.127 8.913 11.061 1 61.11 ? C1 PGW 504 B 1 
HETATM 3 O O01 PGW . . . M 6 -32.96 9.303 11.289 1 64.46 ? O01 PGW 504 B 1 
HETATM 4 C C02 PGW . . . M 6 -32.671 10.768 11.398 1 68.56 ? C02 PGW 504 B 1 
HETATM 5 C C2 PGW . . . M 6 -34.572 8.619 9.651 1 53.76 ? C2 PGW 504 B 1 
HETATM 6 O O02 PGW . . . M 6 -34.977 8.943 11.98 1 61.85 ? O02 PGW 504 B 1 
HETATM 7 C C03 PGW . . . M 6 -31.658 10.996 12.528 1 68.13 ? C03 PGW 504 B 1 
HETATM 8 C C3 PGW . . . M 6 -36.094 8.506 9.639 1 47.79 ? C3 PGW 504 B 1 
HETATM 9 O O03 PGW . . . M 6 -31.413 10.38 9.23 1 81.55 ? O03 PGW 504 B 1 
HETATM 10 C C4 PGW . . . M 6 -36.5 7.182 8.994 1 50.02 ? C4 PGW 504 B 1 
HETATM 11 O O04 PGW . . . M 6 -29.508 10.957 10.09 1 75.59 ? O04 PGW 504 B 1 
HETATM 12 C C5 PGW . . . M 6 -37.986 7.232 8.646 1 42.76 ? C5 PGW 504 B 1 
HETATM 13 C C06 PGW . . . M 6 -40.456 4.895 4.557 1 50.17 ? C06 PGW 504 B 1 
HETATM 14 C C6 PGW . . . M 6 -38.211 6.491 7.328 1 41.92 ? C6 PGW 504 B 1 
HETATM 15 C C07 PGW . . . M 6 -41.304 3.94 3.715 1 45.69 ? C07 PGW 504 B 1 
HETATM 16 C C7 PGW . . . M 6 -37.691 7.333 6.165 1 41.89 ? C7 PGW 504 B 1 
HETATM 17 C C08 PGW . . . M 6 -41.795 4.671 2.464 1 50.84 ? C08 PGW 504 B 1 
HETATM 18 C C8 PGW . . . M 6 -38.475 6.971 4.901 1 53.33 ? C8 PGW 504 B 1 
HETATM 19 C C09 PGW . . . M 6 -43.263 5.065 2.651 1 55.88 ? C09 PGW 504 B 1 
HETATM 20 C C9 PGW . . . M 6 -38.094 5.585 4.442 1 57.27 ? C9 PGW 504 B 1 
HETATM 21 C C10 PGW . . . M 6 -38.998 4.648 4.263 1 56.76 ? C10 PGW 504 B 1 
HETATM 22 C C11 PGW . . . M 6 -44.069 4.668 1.412 1 51.73 ? C11 PGW 504 B 1 
HETATM 23 O O11 PGW . . . M 6 -31.504 12.398 12.777 1 69.4 ? O11 PGW 504 B 1 
HETATM 24 C C15 PGW . . . M 6 -34.982 1.377 9 1 51.39 ? C15 PGW 504 B 1 
HETATM 25 C C16 PGW . . . M 6 -35.768 0.171 8.48 1 51.33 ? C16 PGW 504 B 1 
HETATM 26 C C17 PGW . . . M 6 -35.051 -1.124 8.872 1 51.19 ? C17 PGW 504 B 1 
HETATM 27 C C18 PGW . . . M 6 -36.078 -2.164 9.329 1 60.25 ? C18 PGW 504 B 1 
HETATM 28 C C19 PGW . . . M 6 -30.199 10.137 9.439 1 78.8 ? C19 PGW 504 B 1 
HETATM 29 C C20 PGW . . . M 6 -29.693 8.726 9.271 1 67.37 ? C20 PGW 504 B 1 
HETATM 30 C C21 PGW . . . M 6 -30.362 8.088 8.051 1 72.6 ? C21 PGW 504 B 1 
HETATM 31 C C22 PGW . . . M 6 -30.55 6.587 8.283 1 63.68 ? C22 PGW 504 B 1 
HETATM 32 C C23 PGW . . . M 6 -31.601 6.052 7.307 1 58.2 ? C23 PGW 504 B 1 
HETATM 33 C C24 PGW . . . M 6 -32.888 5.727 8.068 1 54.58 ? C24 PGW 504 B 1 
HETATM 34 C C25 PGW . . . M 6 -33.594 4.543 7.404 1 57.85 ? C25 PGW 504 B 1 
HETATM 35 C C26 PGW . . . M 6 -34.33 3.73 8.473 1 54.4 ? C26 PGW 504 B 1 
HETATM 36 C C27 PGW . . . M 6 -34.816 2.407 7.88 1 50.94 ? C27 PGW 504 B 1 
HETATM 37 C C28 PGW . . . M 6 -35.438 -3.555 9.349 1 52.77 ? C28 PGW 504 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           37 
#